RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16925
(166 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 29.7 bits (67), Expect = 0.068
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 106 DLKNHHNLHTGKRPYTCPWCSRTFAN 131
+L+ H HTG++PY CP C ++F++
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 27.7 bits (62), Expect = 0.31
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 43 KAVHLGERPFVCHECGQSFAS 63
H GE+P+ C CG+SF+S
Sbjct: 6 MRTHTGEKPYKCPVCGKSFSS 26
Score = 25.8 bits (57), Expect = 1.9
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 67 LQEHLTIHSDDAPWKCDICSKK 88
L+ H+ H+ + P+KC +C K
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKS 23
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 28.6 bits (64), Expect = 0.19
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 52 FVCHECGQSFASKGILQEHLTIH 74
+ C ECG+ F SK L+EH+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.1 bits (55), Expect = 3.2
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 120 YTCPWCSRTFANGSNCRSHKRR 141
Y CP C + F + S R H R
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|146952 pfam04560, RNA_pol_Rpb2_7, RNA polymerase Rpb2, domain 7. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). Rpb2 is the
second largest subunit of the RNA polymerase. This
domain comprised of the structural domains anchor and
clamp. The clamp region (C-terminal) contains a
zinc-binding motif. The clamp region is named due to its
interaction with the clamp domain found in Rpb1. The
domain also contains a region termed "switch 4". The
switches within the polymerase are thought to signal
different stages of transcription.
Length = 78
Score = 28.6 bits (65), Expect = 0.40
Identities = 15/57 (26%), Positives = 17/57 (29%), Gaps = 18/57 (31%)
Query: 66 ILQEHLTIHSDDAPWKCDICSKKSLKLSNVSCGWYPDESKDLKNHHNLHTGKRPYTC 122
LQE LTI SDD C C C K + G P +
Sbjct: 21 TLQERLTIKSDDV---CGRC-----GAYAAIC----------KGKTIIEPGDIPESF 59
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 30.5 bits (69), Expect = 0.45
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 43 KAVHLGERPFVCHECGQSFASKGILQEHL-TIHSDDA 78
KA + +VC+ C F+S L EH T HS A
Sbjct: 65 KATPINPSSYVCNVCMAEFSSMDQLAEHQRTTHSIGA 101
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 29.7 bits (66), Expect = 0.80
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 9/77 (11%)
Query: 76 DDAPWKCDI--CSKK-----SLKLSNVS--CGWYPDESKDLKNHHNLHTGKRPYTCPWCS 126
D P+KC + C+KK LK + E+ + + +PY C C
Sbjct: 346 DGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCD 405
Query: 127 RTFANGSNCRSHKRRMH 143
+ + N + + H++ H
Sbjct: 406 KRYKNLNGLKYHRKHSH 422
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 26.1 bits (57), Expect = 1.4
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 120 YTCPWCSRTFANGSNCRSHKRRMH 143
+ CP C ++F++ + H R+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 25.3 bits (55), Expect = 2.5
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 52 FVCHECGQSFASKGILQEHLTIH 74
F C CG+SF+SK L+ HL H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 28.8 bits (64), Expect = 1.4
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 46 HLGERPFVCHECG--QSFASKGILQEHLTIHSDDAPWKCDICSKKSLKLSNVSCG 98
H G + F EC Q++ + LQE LT+ SDD + I SN CG
Sbjct: 1354 HFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECG 1408
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and conversion].
Length = 166
Score = 27.7 bits (62), Expect = 2.2
Identities = 10/38 (26%), Positives = 13/38 (34%), Gaps = 13/38 (34%)
Query: 48 GERPFVCHECGQSFASKGILQEHLTIHSDDAPWKCDIC 85
+ +VC CG H +AP C IC
Sbjct: 131 EGKVWVCPVCG-------------YTHEGEAPEVCPIC 155
>gnl|CDD|136018 PRK06721, PRK06721, threonine synthase; Reviewed.
Length = 352
Score = 28.1 bits (62), Expect = 2.4
Identities = 15/43 (34%), Positives = 17/43 (39%)
Query: 21 GKYSLALMVTRFSSRSAVTAHTKAVHLGERPFVCHECGQSFAS 63
GKY A F R V A KA G +C G + AS
Sbjct: 47 GKYEGANPTGSFKDRGMVMAVAKAKEEGSEAIICASTGNTSAS 89
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 28.0 bits (63), Expect = 2.9
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 121 TCPWCSRTFANGSNCRSHKRRMHPEELK 148
TCP C A G C + R + P EL
Sbjct: 144 TCPKCGGEDARGDQCENCGRTLDPTELI 171
>gnl|CDD|149823 pfam08882, Acetone_carb_G, Acetone carboxylase gamma subunit.
Acetone carboxylase is the key enzyme of bacterial
acetone metabolism, catalyzing the condensation of
acetone and CO(2) to form acetoacetate.
Length = 106
Score = 26.5 bits (59), Expect = 3.3
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 47 LGERPFVCHECGQSFAS-KGILQEHLTIHSDD 77
LG ++C CG F + + I+ D
Sbjct: 11 LGPELWICRVCGHDFGDARENYKLGALIYVRD 42
>gnl|CDD|213729 TIGR02605, CxxC_CxxC_SSSS, putative regulatory protein, FmdB
family. This model represents a region of about 50
amino acids found in a number of small proteins in a
wide range of bacteria. The region begins usually with
the initiator Met and contains two CxxC motifs
separated by 17 amino acids. One member of this family
is has been noted as a putative regulatory protein,
designated FmdB (SP:Q50229, PMID:8841393 ). Most
members of this family have a C-terminal region
containing highly degenerate sequence, such as
SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in
Mycobacterium tuberculosis and
VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces
avermitilis. These low complexity regions, which are
not included in the model, resemble low-complexity
C-terminal regions of some heterocycle-containing
bacteriocin precursors [Regulatory functions, DNA
interactions].
Length = 52
Score = 25.4 bits (56), Expect = 3.8
Identities = 15/47 (31%), Positives = 17/47 (36%), Gaps = 9/47 (19%)
Query: 52 FVCHECGQSFASKGILQEHLTIHSDDAPWKCDICSKKSLK--LSNVS 96
+ C CG F E L SDD C C L+ LS V
Sbjct: 6 YRCTACGHRF-------EVLQKMSDDPLATCPECGSPKLRRLLSAVG 45
>gnl|CDD|234749 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 27.0 bits (61), Expect = 5.3
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 66 ILQEHLTIHSDD 77
LQE LT+ SDD
Sbjct: 1052 TLQEMLTVKSDD 1063
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to be
DNA-binding and may be a transcription factor.
Length = 238
Score = 26.6 bits (59), Expect = 6.1
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 24 SLALMVTRFSSRSAVTAHTKAVH 46
+L R SSRS+ + +A H
Sbjct: 132 TLLDSPRRKSSRSSTVQNKEATH 154
>gnl|CDD|220362 pfam09723, CxxC_CxxC_SSSS, Zinc ribbon domain. This entry
represents a region of about 41 amino acids found in a
number of small proteins in a wide range of bacteria.
The region usually begins with the initiator Met and
contains two CxxC motifs separated by 17 amino acids.
One protein in this entry has been noted as a putative
regulatory protein, designated FmdB. Most proteins in
this entry have a C-terminal region containing highly
degenerate sequence.
Length = 42
Score = 24.5 bits (54), Expect = 7.7
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 7/40 (17%)
Query: 52 FVCHECGQSFASKGILQEHLTIHSDDAPWKCDICSKKSLK 91
+ C +CG +F E L SDD C C ++
Sbjct: 6 YRCEDCGHTF-------EVLQKISDDPLATCPECGSTDVE 38
>gnl|CDD|197903 smart00834, CxxC_CXXC_SSSS, Putative regulatory protein.
CxxC_CXXC_SSSS represents a region of about 41 amino
acids found in a number of small proteins in a wide
range of bacteria. The region usually begins with the
initiator Met and contains two CxxC motifs separated by
17 amino acids. One protein in this entry has been
noted as a putative regulatory protein, designated
FmdB. Most proteins in this entry have a C-terminal
region containing highly degenerate sequence.
Length = 41
Score = 24.1 bits (53), Expect = 7.8
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 7/41 (17%)
Query: 52 FVCHECGQSFASKGILQEHLTIHSDDAPWKCDICSKKSLKL 92
+ C +CG +F E L SDD C C +L
Sbjct: 6 YRCEDCGHTF-------EVLQKISDDPLTTCPECGGDVRRL 39
>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The first LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 57
Score = 24.6 bits (54), Expect = 8.0
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 52 FVCHECGQSFASK 64
F CH+CG+ ASK
Sbjct: 25 FTCHDCGKPVASK 37
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 26.5 bits (59), Expect = 9.1
Identities = 13/76 (17%), Positives = 22/76 (28%), Gaps = 29/76 (38%)
Query: 51 PFV-CHECGQSFASKGILQEHLTIHSDDAPWKCDICSKKSLKLSNVSCGWYPDESKDLKN 109
P + C +CG +C C L+ + L+
Sbjct: 434 PLLLCRDCGYIA-------------------ECPNCDSP---LT------LHKATGQLRC 465
Query: 110 HHNLHTGKRPYTCPWC 125
H+ + P +CP C
Sbjct: 466 HYCGYQEPIPQSCPEC 481
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.133 0.432
Gapped
Lambda K H
0.267 0.0804 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,827,762
Number of extensions: 626075
Number of successful extensions: 597
Number of sequences better than 10.0: 1
Number of HSP's gapped: 595
Number of HSP's successfully gapped: 32
Length of query: 166
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 76
Effective length of database: 6,945,742
Effective search space: 527876392
Effective search space used: 527876392
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (24.8 bits)